SMTL ID : 5ez4.1

2.11 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) P449M/Y450L double mutant from Staphylococcus aureus in complex with NAD+ and BME-modified Cys289

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 27 residues within 4Å: Chain A: I.174, T.175, P.176, W.177, N.178, K.201, P.202, S.203, E.204, G.234, G.238, D.239, F.252, T.253, G.254, G.255, T.258, H.261, I.262, E.276, L.277, G.278, C.310, H.357, K.360, E.411, F.413 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:P.176 Hydrogen bonds: A:T.175, A:N.178, A:K.201, A:E.204, A:G.234, A:D.239, A:D.239, A:G.255, A:T.258, A:T.258, A:E.276, A:K.360, A:E.411 Water bridges: A:G.238, A:I.256, A:T.258, A:K.360 pi-Stacking: A:F.413 NAD.6: 26 residues within 4Å: Chain B: I.174, T.175, P.176, W.177, N.178, K.201, P.202, S.203, E.204, G.234, G.238, D.239, F.252, G.254, G.255, T.258, H.261, I.262, E.276, L.277, G.278, C.310, H.357, K.360, E.411, F.413 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:P.176 Hydrogen bonds: B:T.175, B:N.178, B:K.201, B:E.204, B:G.234, B:D.239, B:G.254, B:G.255, B:G.255, B:E.276, B:K.360, B:E.411, B:E.411 Water bridges: B:G.238, B:I.256, B:I.256, B:T.258, B:T.258, B:K.360, B:K.360 pi-Stacking: B:F.413 NAD.11: 27 residues within 4Å: Chain C: I.174, T.175, P.176, W.177, N.178, K.201, P.202, S.203, E.204, G.234, G.238, D.239, F.252, T.253, G.254, G.255, T.258, H.261, I.262, E.276, L.277, G.278, C.310, H.357, K.360, E.411, F.413 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:P.176 Hydrogen bonds: C:T.175, C:N.178, C:K.201, C:E.204, C:G.234, C:D.239, C:G.254, C:G.254, C:G.255, C:T.258, C:T.258, C:K.360, C:E.411 Water bridges: C:E.204, C:G.238, C:I.256, C:K.360, C:K.360 pi-Stacking: C:F.413 NAD.16: 26 residues within 4Å: Chain D: I.174, T.175, P.176, W.177, N.178, K.201, P.202, S.203, E.204, G.234, G.238, D.239, F.252, G.254, G.255, T.258, H.261, I.262, E.276, L.277, G.278, C.310, H.357, K.360, E.411, F.413 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:P.176 Hydrogen bonds: D:T.175, D:N.178, D:K.201, D:E.204, D:G.234, D:D.239, D:G.254, D:G.255, D:G.255, D:T.258, D:E.276, D:H.357, D:K.360, D:E.411, D:E.411 Water bridges: D:T.258 pi-Stacking: D:F.413

4 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: K.481, G.484, I.485 Chain B: V.270 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.270 NA.7: 3 residues within 4Å: Chain A: V.270 Chain B: K.481, G.484 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.481 NA.12: 3 residues within 4Å: Chain C: K.481, G.484 Chain D: V.270 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.484 Water bridges: D:N.272 NA.17: 4 residues within 4Å: Chain C: V.270 Chain D: K.481, G.484, I.485 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.270 Water bridges: C:N.272

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 3 residues within 4Å: Chain A: Y.179, F.304, H.469 No protein-ligand interaction detected (PLIP) PGE.8: 2 residues within 4Å: Chain B: Y.179, H.469 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.471 PGE.13: 2 residues within 4Å: Chain C: H.469 Chain D: W.514 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.132 PGE.14: 4 residues within 4Å: Chain C: S.363, Y.364, V.367, R.406 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.363, C:R.406, C:R.406 PGE.18: 4 residues within 4Å: Chain D: D.132, Y.179, L.182, H.469 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.132, D:D.132, D:Y.179

5 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 5 residues within 4Å: Chain A: W.38, R.212, E.215, E.218, E.219 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.212, A:E.215, A:E.215 Water bridges: A:R.212, A:E.218 Salt bridges: A:E.215, A:E.215, A:E.218 EPE.5: 9 residues within 4Å: Chain A: N.513, W.514, F.515, S.516, K.517 Chain B: E.124, A.345, T.347, E.348 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.345, A:K.517 Water bridges: B:T.347 Salt bridges: B:E.348 EPE.9: 5 residues within 4Å: Chain B: W.38, R.212, E.215, E.218, E.219 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.212, B:E.215, B:E.219 Water bridges: B:R.212, B:E.219 Salt bridges: B:E.215, B:E.218, B:E.218 EPE.10: 9 residues within 4Å: Chain A: E.124, A.345, T.347, E.348 Chain B: N.513, W.514, F.515, S.516, K.517 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.515, B:K.517 Water bridges: A:T.347 EPE.15: 9 residues within 4Å: Chain C: N.513, W.514, F.515, S.516, K.517 Chain D: E.124, A.345, T.347, E.348 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:F.515, C:K.517, D:A.345 Water bridges: D:T.347

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Halavaty, A.S. et al., 2.11 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) P449M/Y450L double mutant from Staphylococcus aureus in complex with NAD+ and BME-modified Cys289. To Be Published

Release Date

2015-12-09

Peptides

Betaine aldehyde dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Betaine aldehyde dehydrogenase